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One of the major challenges in detecting waterborne pathogens is the low concentration of the target bacteria in water. In this study, we applied the coagulation and foam concentration method to obtain DNA from water samples collected from upstream, near an estuary. The DNA samples were analyzed using 16S rRNA gene sequencing to clarify the microbial community shifts and to identify potentially pathogenic bacteria. Bacterial communities changed as the river flowed downstream, most likely influenced by land use and human activities such as the discharge of wastewater-treatment plant effluent. Based on the 16S rRNA gene amplicon sequencing, potentially pathogenic bacteria were detected with greater than 0.1% of their relative abundances. Among these, Yersinia ruckeri and Pseudomonas alcaligenes were widely detected in the river water. In addition, digital PCR (dPCR) was used to quantify major waterborne pathogens. Shiga toxin-producing Escherichia coli (STEC), Shigella spp., and Campylobacter jejuni were all below the limit of detection. In contrast, general E. coli, which has the beta-D-glucuronidase gene (uidA) were detected by dPCR (copies/100 mL) at similar levels to those measured using the culture-based method (as colony forming units/100 mL). These results suggest that the coagulation and foam concentration method is useful for concentrating microbes and obtaining DNA from river water samples for environmental monitoring.